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Osmoregulation in freshwater anaerobic methane oxidizing archaea under salt stress ISME J. (IF 10.8) Pub Date : 2024-07-20 Maider J Echeveste Medrano, Andy O Leu, Martin Pabst, Yuemei Lin, Simon J Mcllroy, Gene W Tyson, Jitske van Ede, Irene Sánchez-Andrea, Mike S M Jetten, Robert Jansen, Cornelia U Welte
Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at
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Housefly gut microbiomes as a reservoir and facilitator for the spread of antibiotic resistance ISME J. (IF 10.8) Pub Date : 2024-07-18 Dehao Gan, Zhenyan Lin, Lingshuang Zeng, Hui Deng, Timothy R Walsh, Shungui Zhou, Qiu E Yang
Arthropods, such as houseflies, play a significant role on the dissemination of antimicrobial resistance (AMR); however, their impact has often been overlooked in comparison to other AMR vectors. Understanding the contribution of arthropods to the spread of AMR is critical for implementing robust policies to mitigate the spread of AMR across “One Health” sectors. Herein, we investigated the in-situ
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Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions ISME J. (IF 10.8) Pub Date : 2024-07-18 Bailey A Wallace, Natascha S Varona, Poppy J Hesketh-Best, Alexandra K Stiffler, Cynthia B Silveira
Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacteria-host interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment
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Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome ISME J. (IF 10.8) Pub Date : 2024-07-17 Adrián López-Beltrán, João Botelho, Jaime Iranzo
Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals
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Molecular basis of phenotypic plasticity in a marine ciliate ISME J. (IF 10.8) Pub Date : 2024-07-17 Jiao Pan, Yaohai Wang, Chao Li, Simo Zhang, Zhiqiang Ye, Jiahao Ni, Haichao Li, Yichen Li, Hongwei Yue, Chenchen Ruan, Dange Zhao, Yujian Jiang, Xiaolin Wu, Xiaopeng Shen, Rebecca A Zufall, Yu Zhang, Weiyi Li, Michael Lynch, Hongan Long
Phenotypic plasticity, which involves phenotypic transformation in the absence of genetic change, may serve as a strategy for organisms to survive in complex and highly-fluctuating environments. However, its reaction norm, molecular basis, and evolution remain unclear in most organisms, especially microbial eukaryotes. In this study, we explored these questions by investigating the reaction norm, regulation
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Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution ISME J. (IF 10.8) Pub Date : 2024-07-12 Tom A Williams, Adrian A Davin, Lénárd L Szánthó, Alexandros Stamatakis, Noah A Wahl, Ben J Woodcroft, Rochelle M Soo, Laura Eme, Paul O Sheridan, Cecile Gubry-Rangin, Anja Spang, Philip Hugenholtz, Gergely J Szöllősi
In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying
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Distinctive chemotactic responses of three marine herbivore protists to DMSP and related compounds ISME J. (IF 10.8) Pub Date : 2024-07-11 Queralt Güell-Bujons, Medea Zanoli, Idan Tuval, Albert Calbet, Rafel Simó
Marine planktonic predator–prey interactions occur in microscale seascapes, where diffusing chemicals may act either as chemotactic cues that enhance or arrest predation, or as elemental resources that are complementary to prey ingestion. The phytoplankton osmolyte dimethylsulfoniopropionate (DMSP) and its degradation products dimethylsulfide (DMS) and acrylate are pervasive compounds with high chemotactic
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Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability ISME J. (IF 10.8) Pub Date : 2024-07-11 Yanfeng Zhao, Alina Bitzer, Jeffrey John Power, Darya Belikova, Benjamin Orlando Torres Salazar, Lea Antje Adolf, David Leon Gerlach, Bernhard Krismer, Simon Heilbronner
The human microbiome is critically associated with human health and disease. One aspect of this is that antibiotic-resistant opportunistic bacterial pathogens such as methicillin-resistant Staphylococcus aureus can reside within the nasal microbiota which increases the risk of infections. Epidemiological studies of the nasal microbiome have revealed positive and negative correlations between non-pathogenic
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Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat ISME J. (IF 10.8) Pub Date : 2024-07-11 Tessa E Reid, Vanessa N Kavamura, Adriana Torres-Ballesteros, Monique E Smith, Maïder Abadie, Mark Pawlett, Ian M Clark, Jim A Harris, Tim H Mauchline
The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification have been limited. This study investigated how endogenous (genome polyploidization), and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture -independent and -dependent
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Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis ISME J. (IF 10.8) Pub Date : 2024-07-11 Amirhossein Gheitanchi Mashini, Clinton A Oakley, Lifeng Peng, Arthur R Grossman, Virginia M Weis, Simon K Davy
Cellular mechanisms responsible for the regulation of nutrient exchange, immune responses, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved, particularly with respect to the dinoflagellate symbiont. Here, we characterised proteomic changes in the native symbiont Breviolum minutum during colonisation of its host sea anemone Exaiptasia diaphana (“Aiptasia”)
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Linking active rectal mucosa-attached microbiota to host immunity reveals its role in host-pathogenic STEC O157 interactions ISME J. (IF 10.8) Pub Date : 2024-07-10 Zhe Pan, Yanhong Chen, Mi Zhou, Tim A McAllister, Tom N Mcneilly, Le Luo Guan
The rectal anal junction (RAJ) is the major colonization site of Shiga toxin-producing Escherichia coli (STEC) O157 in beef cattle, leading to transmission of this foodborne pathogen from farms to food chains. To date, there is limited understanding on whether mucosa-attached microbiome has a profound impact on host-STEC interactions. In this study, the active RAJ mucosa-attached microbiota and its
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Defined synthetic microbial communities colonize and benefit field-grown sorghum ISME J. (IF 10.8) Pub Date : 2024-07-10 Citlali Fonseca-García, Dean Pettinga, Andrew Wilson, Joshua R Elmore, Ryan McClure, Jackie Atim, Julie Pedraza, Robert Hutmacher, Halbay Turumtay, Yang Tian, Aymerick Eudes, Henrik V Scheller, Robert Egbert, Devin Coleman-Derr
The rhizosphere constitutes a dynamic interface between plant hosts and their associated microbial communities. Despite the acknowledged potential for enhancing plant fitness by manipulating the rhizosphere, the engineering of the rhizosphere microbiome through inoculation has posed significant challenges. These challenges are thought to arise from the competitive microbial ecosystem where introduced
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Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles ISME J. (IF 10.8) Pub Date : 2024-07-08 Yohei Nishikawa, Ryota Wagatsuma, Yuko Tsukada, Lin Chia-ling, Rieka Chijiiwa, Masahito Hosokawa, Haruko Takeyama
Environmental viruses (primarily bacteriophages) are widely recognized as playing an important role in ecosystem homeostasis through the infection of host cells. However, the majority of environmental viruses are still unknown as their mosaic structure and frequent mutations in their sequences hinder genome construction in current metagenomics. To enable the large-scale acquisition of environmental
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Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts ISME J. (IF 10.8) Pub Date : 2024-07-06 Anna Schrecengost, Johana Rotterová, Kateřina Poláková, Ivan Čepička, Roxanne A Beinart
Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the
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Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria ISME J. (IF 10.8) Pub Date : 2024-07-03 Matthias Hoetzinger, Martin W Hahn, Linnéa Y Andersson, Nathaniel Buckley, Chelsea Ramsin, Moritz Buck, Julia K Nuy, Sarahi L Garcia, Fernando Puente-Sánchez, Stefan Bertilsson
Implications of geographic separation and temporal dynamics on the evolution of free-living bacterial species are widely unclear. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world provides an unprecedented opportunity for such investigations. Here we exploited publicly available and new freshwater metagenomes in combination
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Type IV secretion system effector sabotages multiple defense systems in a competing bacterium ISME J. (IF 10.8) Pub Date : 2024-07-03 Bingxin Wang, Fugui Xu, Zeyu Zhang, Danyu Shen, Limin Wang, Huijun Wu, Qing Yan, Chuanbin Cui, Pingping Wang, Qi Wei, Xiaolong Shao, Mengcen Wang, Guoliang Qian
Effector proteins secreted by bacteria that infect mammalian and plant cells often subdue eukaryotic host cell defenses by simultaneously affecting multiple targets. However, instances when a bacterial effector injected in the competing bacteria sabotage more than a single target have not been reported. Here, we demonstrate that the effector protein, LtaE, translocated by the type IV secretion system
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Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health ISME J. (IF 10.8) Pub Date : 2024-07-02 Sang-Moo Lee, Roniya Thapa Magar, Min Kyeong Jung, Hyun Gi Kong, Ju Yeon Song, Joo Hwan Kwon, Minseo Choi, Hyoung Ju Lee, Seung Yeup Lee, Raees Khan, Jihyun F Kim, Seon-Woo Lee
Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remains poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp
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Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates ISME J. (IF 10.8) Pub Date : 2024-06-25 Qi Song, Fangqing Zhao, Lina Hou, Miao Miao
As unicellular predators, ciliates engage in close associations with diverse microbes, laying the foundation for the establishment of endosymbiosis. Originally heterotrophic, ciliates demonstrate the ability to acquire phototrophy by phagocytizing unicellular algae or by sequestering algal plastids. This adaptation enables them to gain photosynthate and develop resistance to unfavorable environmental
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Interspecies ecological competition rejuvenates decayed Geobacter electroactive biofilm ISME J. (IF 10.8) Pub Date : 2024-06-25 Yin Ye, Lu Zhang, Xiaohui Hong, Man Chen, Xing Liu, Shungui Zhou
Bioelectrochemical systems (BESs) exploit electroactive biofilms (EABs) for promising applications in biosensing, wastewater treatment, energy production and chemical biosynthesis. However, during the operation of BESs, EABs inevitably decay. Seeking approaches to rejuvenate decayed EABs is critical for the sustainability and practical application of BESs. Prophage induction has been recognized as
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Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments ISME J. (IF 10.8) Pub Date : 2024-06-25 Shasha Wang, Lijing Jiang, Zhuoming Zhao, Zhen Chen, Jun Wang, Karine Alain, Liang Cui, Yangsheng Zhong, Yongyi Peng, Qiliang Lai, Xiyang Dong, Zongze Shao
Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. So far chemolithoautotrophic bacteria are widely recognized as the principal diazotrophs in oligotrophic marine and terrestrial ecosystems. However, the contribution of chemolithoautotrophs to nitrogen fixation in organic-rich habitats remains unclear. Here, we utilized metagenomic and metatranscriptomic approaches
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Aerobic denitrification as an N2O source from microbial communities ISME J. (IF 10.8) Pub Date : 2024-06-24 Nina Roothans, Minke Gabriëls, Thomas Abeel, Martin Pabst, Mark C M van Loosdrecht, Michele Laureni
Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed
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Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders ISME J. (IF 10.8) Pub Date : 2024-06-24 Jibing Li, Chunling Luo, Xixi Cai, Dayi Zhang, Guoqing Guan, Bei Li, Gan Zhang
Soil microbial flora constitutes a highly diverse and complex microbiome on Earth, often challenging to cultivation, with unclear metabolic mechanisms in situ. Here, we present a pioneering concept for the in situ construction of functional microbial consortia (FMCs) and introduce an innovative method for creating FMCs by utilising phenanthrene as a model compound to elucidate their in situ biodegradation
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Island biogeography theory provides a plausible explanation for why larger vertebrates and taller humans have more diverse gut microbiomes ISME J. (IF 10.8) Pub Date : 2024-06-20 Katherine Ramos Sarmiento, Alex Carr, Christian Diener, Kenneth J Locey, Sean M Gibbons
Prior work has shown a positive scaling relationship between vertebrate body size, human height, and gut microbiome alpha diversity. This observation mirrors commonly observed species area relationships (SAR) in many other ecosystems. Here, we expand these observations to several large data sets, showing that this size-diversity scaling relationship is independent of relevant covariates, like diet
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Microbially mediated sulfur oxidation coupled with arsenate reduction within oligotrophic mining-impacted habitats ISME J. (IF 10.8) Pub Date : 2024-06-20 Xiaoxu Sun, Qizhi Chen, Max M Häggblom, Guoqiang Liu, Tianle Kong, Duanyi Huang, Zhenyu Chen, Fangbai Li, Baoqin Li, Weimin Sun
Arsenate reduction is a major cause of As release from soils which threatens more than 200 million people worldwide. While heterotrophic As(V) reduction has been investigated extensively, the mechanism of chemolithotrophic As(V) reduction is less studied. Since As is frequently found as sulfidic minerals in the environment, microbial mediated sulfur oxidation coupled to As(V) reduction (SOAsR), a chemolithotrophic
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Intracellular symbiont Symbiodolus is vertically transmitted and widespread across insect orders ISME J. (IF 10.8) Pub Date : 2024-06-14 Jürgen C Wierz, Philipp Dirksen, Roy Kirsch, Ronja Krüsemer, Benjamin Weiss, Yannick Pauchet, Tobias Engl, Martin Kaltenpoth
Insects engage in manifold interactions with bacteria that can shift along the parasitism–mutualism continuum. However, only a small number of bacterial taxa managed to successfully colonize a wide diversity of insects, by evolving mechanisms for host-cell entry, immune evasion, germline tropism, reproductive manipulation, and/or by providing benefits to the host that stabilize the symbiotic association
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Genome-wide screen of genetic determinants that govern Escherichia coli growth and persistence in lake water ISME J. (IF 10.8) Pub Date : 2024-06-14 Nataliya Teteneva, Ananda Sanches-Medeiros, Victor Sourjik
Although enteric bacteria normally reside within the animal intestine, the ability to persist extraintestinally is an essential part of their overall lifestyle, and it might contribute to transmission between hosts. Despite this potential importance, few genetic determinants of extraintestinal growth and survival have been identified, even for the best-studied model, Escherichia coli. In this work
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Resistance towards and biotransformation of a Pseudomonas-produced secondary metabolite during community invasion ISME J. (IF 10.8) Pub Date : 2024-06-13 Morten L Hansen, Zsófia Dénes, Scott A Jarmusch, Mario Wibowo, Carlos N Lozano-Andrade, Ákos T Kovács, Mikael L Strube, Aaron J C Andersen, Lars Jelsbak
The role of antagonistic secondary metabolites produced by Pseudomonas protegens in suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability of P. protegens to establish in soil and rhizosphere microbiomes remains less clear. Here, we use a four-species synthetic community (SynCom) in which individual members are sensitive towards key P. protegens
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Nonparametric richness estimators Chao1 and ACE must not be used with amplicon sequence variant data ISME J. (IF 10.8) Pub Date : 2024-06-12 Yongcui Deng, Alexander K Umbach, Josh D Neufeld
Microbial ecologists use alpha diversity metrics for estimating species richness and evenness from data obtained by high-throughput sequencing of small subunit ribosomal RNA genes. This perspective argues that the nonparametric richness estimators Chao1 and ACE should never be used with ASV data because the default process of generating amplicon sequence variants (ASVs) removes singletons, which are
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Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption ISME J. (IF 10.8) Pub Date : 2024-06-11 Falk Eigemann, Karen Tait, Ben Temperton, Ferdi L Hellweger
Molecular observational tools are great for characterizing the composition and genetic endowment of microbial communities, but cannot measure fluxes, which are critical for the understanding of ecosystems. To overcome these limitations, we use a mechanistic inference approach to estimate dissolved organic carbon (DOC) production and consumption by phytoplankton operational taxonomic units (OTUs) and
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Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders ISME J. (IF 10.8) Pub Date : 2024-06-11 Owen G Osborne, Randall R Jiménez, Allison Q Byrne, Brian Gratwicke, Amy Ellison, Carly R Muletz-Wolz
Phylosymbiosis is an association between host-associated microbiome composition and host phylogeny. This pattern can arise via evolution of host traits, habitat preferences, diets, and co-diversification of hosts and microbes. Understanding the drivers of phylosymbiosis is vital for modelling disease-microbiome interactions and manipulating microbiomes in multi-host systems. This study quantifies phylosymbiosis
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Pectin supplementation accelerates post-antibiotic gut microbiome reconstitution orchestrated with reduced gut redox potential ISME J. (IF 10.8) Pub Date : 2024-06-10 Rongying Xu, Ni Feng, Qiuke Li, Hongyu Wang, Lian Li, Xiaobo Feng, Yong Su, Weiyun Zhu
Antibiotic-induced gut dysbiosis (AID) is a big challenge for host health, and the recovery from this dysbiosis is often slow and incomplete. AID is typically featured by elevation in redox potential, Enterobacteriaceae load, and aerobic metabolism. In our previous study, pectin-enriched diet could decrease fecal redox potential and modulate gut microbiome. Therefore, we propose that pectin supplementation
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Leveraging genome-scale metabolic models to understand aerobic methanotrophs ISME J. (IF 10.8) Pub Date : 2024-06-10 Magdalena Wutkowska, Vojtěch Tláskal, Sergio Bordel, Lisa Y Stein, Justus Amuche Nweze, Anne Daebeler
Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidisers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high
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Evolutionary history of tyrosine-supplementing endosymbionts in pollen-feeding beetles ISME J. (IF 10.8) Pub Date : 2024-06-08 Jürgen C Wierz, Matthew L Gimmel, Selina Huthmacher, Tobias Engl, Martin Kaltenpoth
Many insects feeding on nutritionally challenging diets like plant sap, leaves, or wood engage in ancient associations with bacterial symbionts that supplement limiting nutrients or produce digestive or detoxifying enzymes. However, the distribution, function, and evolutionary dynamics of microbial symbionts in insects exploiting other plant tissues or relying on a predacious diet remain poorly understood
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Metabolite cross-feeding enables concomitant catabolism of chlorinated methanes and chlorinated ethenes in synthetic microbial assemblies ISME J. (IF 10.8) Pub Date : 2024-05-31 Gao Chen, Yi Yang, Jun Yan, Frank E Löffler
Isolate studies have been a cornerstone for unravelling metabolic pathways and phenotypical (functional) features. Biogeochemical processes in natural and engineered ecosystems are generally performed by more than a single microbe and often rely on mutualistic interactions. We demonstrate the rational bottom-up design of synthetic, interdependent co-cultures to achieve concomitant utilization of chlorinated
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Lytic and temperate phage naturally coexist in a dynamic population model ISME J. (IF 10.8) Pub Date : 2024-05-31 Ofer Kimchi, Yigal Meir, Ned S Wingreen
When phage infect their bacterial hosts, they may either lyse the cell and generate a burst of new phage, or lysogenize the bacterium, incorporating the phage genome into it. Phage lysis/lysogeny strategies are assumed to be highly optimized, with the optimal tradeoff depending on environmental conditions. However, in nature, phage of radically different lysis/lysogeny strategies coexist in the same
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The atmosphere: a transport medium or an active microbial ecosystem? ISME J. (IF 10.8) Pub Date : 2024-05-28 Rachael Lappan, Jordan Thakar, Laura Molares Moncayo, Alexi Besser, James A Bradley, Jacqueline Goordial, Elizabeth Trembath-Reichert, Chris Greening
The atmosphere may be Earth’s largest microbial ecosystem. It is connected to all of Earth’s surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another
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Microbial ecology of the deep terrestrial subsurface ISME J. (IF 10.8) Pub Date : 2024-05-23 Rachel C Beaver, Josh D Neufeld
The terrestrial subsurface hosts diverse microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, contemporary research demonstrates that deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important
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Symbiotic bacteria and fungi proliferate in diapause and may enhance overwintering survival in a solitary bee ISME J. (IF 10.8) Pub Date : 2024-05-20 Shawn M Christensen, Sriram Srinivas, Quinn S McFrederick, Bryan N Danforth, Stephen L Buchmann, Rachel L Vannette
Host–microbe interactions underlie the development and fitness of many macroorganisms, including bees. Whereas many social bees benefit from vertically transmitted gut bacteria, current data suggests that solitary bees, which comprise the vast majority of species diversity within bees, lack a highly specialized gut microbiome. Here we examine the composition and abundance of bacteria and fungi throughout
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Warming effects on grassland soil microbial communities are amplified in cool months ISME J. (IF 10.8) Pub Date : 2024-05-14 Jiesi Lei, Yuanlong Su, Siyang Jian, Xue Guo, Mengting Yuan, Colin T Bates, Zhou Jason Shi, Jiabao Li, Yifan Su, Daliang Ning, Liyou Wu, Jizhong Zhou, Yunfeng Yang
Global warming modulates soil respiration (RS) via microbial decomposition, which is seasonally dependent. Yet, the magnitude and direction of this modulation remain unclear, partly owing to the lack of knowledge on how microorganisms respond to seasonal changes. Here, we investigated the temporal dynamics of soil microbial communities over 12 consecutive months under experimental warming in a tallgrass
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Metabolic potential of Nitrososphaera-associated clades ISME J. (IF 10.8) Pub Date : 2024-05-14 Qicheng Bei, Thomas Reitz, Martin Schädler, Logan H Hodgskiss, Jingjing Peng, Beatrix Schnabel, François Buscot, Nico Eisenhauer, Christa Schleper, Anna Heintz-Buschart
Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180
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Active prophages in coral-associated Halomonas capable of lateral transduction ISME J. (IF 10.8) Pub Date : 2024-05-13 Ziyao Liu, Kaihao Tang, Yiqing Zhou, Tianlang Liu, Yunxue Guo, Duoting Wu, Xiaoxue Wang
Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated
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Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming ISME J. (IF 10.8) Pub Date : 2024-05-09 Andrea Söllinger, Laureen S Ahlers, Mathilde Borg Dahl, Páll Sigurðsson, Coline Le Noir de Carlan, Biplabi Bhattarai, Christoph Gall, Victoria S Martin, Cornelia Rottensteiner, Liabo L Motleleng, Eva Marie Breines, Erik Verbruggen, Ivika Ostonen, Bjarni D Sigurdsson, Andreas Richter, Alexander T Tveit
Physiological responses of soil microorganisms to global warming are important for soil ecosystem function and the terrestrial carbon cycle. Here, we investigate the effects of weeks, years, and decades of soil warming across seasons and time on the microbial protein biosynthesis machineries (i.e. ribosomes), the most abundant cellular macromolecular complexes, using RNA:DNA and RNA:MBC (microbial
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Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures ISME J. (IF 10.8) Pub Date : 2024-05-08 Wei Li, David Baliu-Rodriguez, Sanduni H Premathilaka, Sharmila I Thenuwara, Jeffrey A Kimbrel, Ty J Samo, Christina Ramon, E Anders Kiledal, Sara R Rivera, Jenan Kharbush, Dragan Isailovic, Peter K Weber, Gregory J Dick, Xavier Mayali
Nutrient-induced blooms of the globally abundant freshwater toxic cyanobacterium Microcystis cause worldwide public and ecosystem health concerns. The response of Microcystis growth and toxin production to new and recycled nitrogen (N) inputs, and the impact of heterotrophic bacteria in the Microcystis phycosphere on these processes are not well understood. Here, using microbiome transplant experiments
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Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments ISME J. (IF 10.8) Pub Date : 2024-05-06 Jiulong Zhao, Shailesh Nair, Zenghu Zhang, Zengmeng Wang, Nianzhi Jiao, Yongyu Zhang
The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing
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Enantioselective transformation of phytoplankton-derived dihydroxypropanesulfonate by marine bacteria ISME J. (IF 10.8) Pub Date : 2024-05-06 Le Liu, Xiang Gao, Changjie Dong, Huanyu Wang, Xiaofeng Chen, Xiaoyi Ma, Shujing Liu, Quanrui Chen, Dan Lin, Nianzhi Jiao, Kai Tang
Chirality, a fundamental property of matter, is often overlooked in the studies of marine organic matter cycles. Dihydroxypropanesulfonate (DHPS), a globally abundant organosulfur compound, serves as an ecologically important currency for nutrient and energy transfer from phytoplankton to bacteria in the ocean. However, the chirality of DHPS in nature and its transformation remain unclear. Here, we
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Deazaflavin metabolite produced by endosymbiotic bacteria controls fungal host reproduction ISME J. (IF 10.8) Pub Date : 2024-05-01 Ingrid Richter, Mahmudul Hasan, Johannes W Kramer, Philipp Wein, Jana Krabbe, K Philip Woitas, Timothy P Stinear, Sacha J Pidot, Florian Kloss, Christian Hertweck, Gerald Lackner
The endosymbiosis between the pathogenic fungus Rhizopus microsporus and the toxin-producing bacterium Mycetohabitans rhizoxinica represents a unique example of host control by an endosymbiont. Fungal sporulation strictly depends on the presence of endosymbionts as well as bacterially produced secondary metabolites. However, an influence of primary metabolites on host control remained unexplored. Recently
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Depletion of protective microbiota promotes the incidence of fruit disease ISME J. (IF 10.8) Pub Date : 2024-05-01 Xue Luo, Kai Sun, Hao-Ran Li, Xiang-Yu Zhang, Yi-Tong Pan, De-Lin Luo, Yi-Bo Wu, Hui-Jun Jiang, Xiao-Han Wu, Chen-Yu Ma, Chuan-Chao Dai, Wei Zhang
Plant-associated microbiomes play important roles in plant health and productivity. However, despite fruits being directly linked to plant productivity, little is known about the microbiomes of fruits and their potential association with fruit health. Here, by integrating 16S rRNA gene, ITS high-throughput sequencing data and microbiological culturable approaches, we reported that roots and fruits
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Distinct life cycle stages of an ectosymbiotic DPANN archaeon ISME J. (IF 10.8) Pub Date : 2024-05-01 Vasil A Gaisin, Marleen van Wolferen, Sonja-Verena Albers, Martin Pilhofer
DPANN archaea are a diverse group of microorganisms that are thought to rely on an ectosymbiotic lifestyle; however, the cell biology of these cell–cell interactions remains largely unknown. We applied live-cell imaging and cryo-electron tomography to the DPANN archaeon Nanobdella aerobiophila and its host, revealing two distinct life cycle stages. Free cells possess archaella and are motile. Ectobiotic
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Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence ISME J. (IF 10.8) Pub Date : 2024-05-01 Etthel M Windels, Lloyd Cool, Eline Persy, Janne Swinnen, Paul Matthay, Bram Van den Bergh, Tom Wenseleers, Jan Michiels
Effective treatment of bacterial infections proves increasingly challenging due to the emergence of bacterial variants that endure antibiotic exposure. Antibiotic resistance and persistence have been identified as two major bacterial survival mechanisms, and several studies have shown a rapid and strong selection of resistance or persistence mutants under repeated drug treatment. Yet, little is known
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Mechanisms and implications of bacterial-fungal competition for soil resources ISME J. (IF 10.8) Pub Date : 2024-05-01 Chaoqun Wang, Yakov Kuzyakov
Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, and functions in soil, as well as regulate carbon (C) and nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources is the main factor determining the adaptation and niche differentiation between these two big microbial
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Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism ISME J. (IF 10.8) Pub Date : 2024-05-01 Xianyi Xiong, Hans G Othmer, William R Harcombe
Antibiotic persistence (heterotolerance) allows a sub-population of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial
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Proton-pumping rhodopsins promote the growth and survival of phytoplankton in a highly variable ocean ISME J. (IF 10.8) Pub Date : 2024-04-30 William G Sunda, Adrian Marchetti
Proton-pumping rhodopsins (PPRs) utilize sunlight to produce cellular energy. They are widely distributed in marine phytoplankton and were recently shown to occur in the vacuolar membrane of a marine diatom, making the vacuole a second light transducing organelle. Of course, the first, the chloroplast, is where photosynthesis occurs. However, the two light-driven sources of cellular energy are quite
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Siderophores and competition for iron govern myxobacterial predation dynamics ISME J. (IF 10.8) Pub Date : 2024-04-29 Francisco Javier Contreras-Moreno, Aurelio Moraleda-Muñoz, Francisco Javier Marcos-Torres, Virginia Cuéllar, María José Soto, Juana Pérez, José Muñoz-Dorado
Bacterial predators are decisive organisms that shape microbial ecosystems. In this study, we investigated the role of iron and siderophores during the predatory interaction between two rhizosphere bacteria: Myxococcus xanthus, an epibiotic predator, and Sinorhizobium meliloti, a bacterium that establishes nitrogen-fixing symbiosis with legumes. The results show that iron enhances the motility of the
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Rhizobium determinants of rhizosphere persistence and root colonisation ISME J. (IF 10.8) Pub Date : 2024-04-26 Hayley E Knights, Vinoy K Ramachandran, Beatriz Jorrin, Raphael Ledermann, Jack D Parsons, Samuel T N Aroney, Philip S Poole
Bacterial persistence in the rhizosphere and colonisation of root niches are critical for the establishment of many beneficial plant-bacteria interactions including those between Rhizobium leguminosarum and its host legumes. Despite this, most studies on R. leguminosarum have focused on its symbiotic lifestyle as an endosymbiont in root nodules. Here, we use random barcode transposon sequencing (RB-TnSeq)
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Bridging ecological assembly process and community stability upon bacterial invasions ISME J. (IF 10.8) Pub Date : 2024-04-25 Xipeng Liu, Joana Falcão Salles
Understanding the link between microbial community stability and assembly processes is crucial in microbial ecology. Here, we investigated whether the impact of biotic disturbances would depend on the processes controlling community assembly. For that, we performed an experiment using soil microcosms in which microbial communities assembled through different processes were invaded by Escherichia coli
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Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates ISME J. (IF 10.8) Pub Date : 2024-04-24 Sarah Shah, Katherine E Dougan, Yibi Chen, Rosalyn Lo, Gemma Laird, Michael D A Fortuin, Subash K Rai, Valentine Murigneux, Anthony J Bellantuono, Mauricio Rodriguez-Lanetty, Debashish Bhattacharya, Cheong Xin Chan
Dinoflagellates in the family Symbiodiniaceae are taxonomically diverse, predominantly symbiotic lineages that are well-known for their association with corals. The ancestor of these taxa is believed to have been free-living. The establishment of symbiosis (i.e., symbiogenesis) is hypothesised to have occurred multiple times during Symbiodiniaceae evolution, but its impact on genome evolution of these
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Co-occurring nitrifying symbiont lineages are vertically inherited and widespread in marine sponges ISME J. (IF 10.8) Pub Date : 2024-04-23 Bettina Glasl, Heidi M Luter, Katarina Damjanovic, Katharina Kitzinger, Anna J Mueller, Leonie Mahler, Joan Pamela Engelberts, Laura Rix, Jay T Osvatic, Bela Hausmann, Joana Séneca, Holger Daims, Petra Pjevac, Michael Wagner
Ammonia-oxidising archaea and nitrite-oxidising bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification - the aerobic oxidation of ammonia to nitrite and further to nitrate - and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterise two novel nitrifying symbiont
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Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates ISME J. (IF 10.8) Pub Date : 2024-04-22 Zoila I Alvarez-Aponte, Alekhya M Govindaraju, Zachary F Hallberg, Alexa M Nicolas, Myka A Green, Kenny C Mok, Citlali Fonseca-Garcia, Devin Coleman-Derr, Eoin L Brodie, Hans K Carlson, Michiko E Taga
Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions
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Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments ISME J. (IF 10.8) Pub Date : 2024-04-22 Dilem Ruhluel, Lewis Fisher, Thomas E Barton, Hollie Leighton, Sumit Kumar, Paula Amores Morillo, Siobhan O’Brien, Joanne L Fothergill, Daniel R Neill
Pseudomonas aeruginosa is a cause of chronic respiratory tract infections in people with cystic fibrosis (CF), non-CF bronchiectasis and chronic obstructive pulmonary disease. Prolonged infection allows accumulation of mutations and horizontal gene transfer, increasing the likelihood of adaptive phenotypic traits. Adaptation is proposed to arise first in bacterial populations colonising upper airway
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Ecological relevance of flagellar motility in soil bacterial communities ISME J. (IF 10.8) Pub Date : 2024-04-22 Josep Ramoneda, Kunkun Fan, Jane M Lucas, Haiyan Chu, Andrew Bissett, Michael S Strickland, Noah Fierer
Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility